from ARM-USB-TINY-H specification,
it supports ARM targets working in voltage range 2.0 - 5.0 V DC
but when using VREF=2.5V (2.5V target VDD connected to pin 1 & 2),
ARM-USB-TINY-H output 3.3V clock signal on TCK (pin 9).
so it seems to not translate voltage according to VREF level,
resulting of target JTAG input electrical overstress.
could you confirm that ARM-USB-TINY-H drive only 3.3V target ?
What you measured is correct but this doesn't mean it will not work. ARM-USB-TINY-H works from 2V to 5V. In one direction the FTDI chip works from 2V to 5V. In the other there are resistors. While the resistors are not the best solution they are good enough for research and development work.
If you want voltage translation between the debugger and the target's VREF, consider ARM-USB-OCD-H. It is equipped with dual-bit dual-supply bus transceivers with configurable voltage translation. Then if you have 2.5V at VREF, you would measure 2.5V at TCK.